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Table 4 Area under the curve for the differential expression

From: Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching

Alignment and count method Exact test Log ratio T-test-log
STAR-countOverlaps 0.917 0.9191 0.8845
tophat-countOverlaps 0.9162 0.9183 0.8837
STAR-htseq 0.9119 0.916 0.8797
tophat-htseq 0.9109 0.9151 0.8784
RSEM-TPM 0.9264 0.9342 0.8964
RSEM-posteriorTPM 0.9273 0.9355 0.897
RSEM-count 0.9295 0.9328 0.8959
RSEM-posteriorCount 0.9303 0.9338 0.8965
  1. The table shows the overall AUC value for the detection of differential expression. The samples were designed such that each gene was differentially expressed in multiple comparisons. Using different types of input we apply 3 testing scores: exactTest (edgeR package), log-ratio (as an example for effect-size estimation), t-test on the log-expression scores (as a baseline in order to contrast the benefit of using a count-model).